Merge branch 'main' into doc/change_to_entity

Author: tien-tong

cubids/cli.py

@@ -17,17 +17,48 @@
 
 
 def _path_exists(path, parser):
-    """Ensure a given path exists."""
-    if path is None or not Path(path).exists():
-        raise parser.error(f"Path does not exist: <{path}>.")
-    return Path(path).absolute()
+    """Ensure a given path exists.
+
+    Parameters
+    ----------
+    path : str
+        Path to check for existence.
+    parser : argparse.ArgumentParser
+        Argument parser object.
+
+    Returns
+    -------
+    pathlib.Path
+        Absolute path to the given location.
+    """
+    if path is not None:
+        path = Path(path)
+
+    if path is None or not path.exists():
+        raise parser.error(f"Path does not exist: <{path.absolute()}>.")
+    return path.absolute()
 
 
 def _is_file(path, parser):
-    """Ensure a given path exists and it is a file."""
+    """Ensure a given path exists and it is a file.
+
+    Parameters
+    ----------
+    path : str
+        Path to check for existence.
+    parser : argparse.ArgumentParser
+        Argument parser object.
+
+    Returns
+    -------
+    pathlib.Path
+        Absolute path to the given location.
+    """
     path = _path_exists(path, parser)
     if not path.is_file():
-        raise parser.error(f"Path should point to a file (or symlink of file): <{path}>.")
+        raise parser.error(
+            f"Path should point to a file (or symlink of file): <{path.absolute()}>."
+        )
     return path
 
 

cubids/tests/test_cli.py

@@ -1,83 +1,102 @@
-"""
-This file contains unit tests for the command-line interface (CLI) of the CuBIDS package.
+"""Unit tests for the command-line interface (CLI) of the CuBIDS package.
 
 The tests cover the following functions:
 - _path_exists: Tests whether a given path exists or not.
 - _is_file: Tests whether a given path is a file or a directory.
-- _get_parser: Tests the creation and configuration of the argument parser.
-- _main: Tests the main function of the CLI.
 
 Each test case includes assertions to verify the expected behavior of the corresponding function.
-
-Author: [Your Name]
-Date: [Current Date]
 """
 
 import argparse
+from functools import partial
 
 import pytest
 
-from cubids.cli import _get_parser, _is_file, _main, _path_exists
-
-
-def _test_path_exists():
-    """Test whether a given path exists or not.
-
-    This function tests the `_path_exists` function by providing a path that exists
-    and a path that does not exist.
-    It asserts that the function returns the expected path when the path exists,
-    and raises an `argparse.ArgumentTypeError` when the path does not exist.
-    """
-    assert _path_exists("/path/to/existing/file", None) == "/path/to/existing/file"
-
-    with pytest.raises(argparse.ArgumentTypeError):
-        _path_exists("/path/to/nonexistent/file", None)
-
-
-def _test_is_file():
-    """Test whether a given path is a file or a directory.
-
-    This function tests the `_is_file` function by providing a path that is a file
-    and a path that is a directory.
-    It asserts that the function returns the expected path when the path is a file,
-    and raises an `argparse.ArgumentTypeError` when the path is a directory.
-    """
-    assert _is_file("/path/to/file.txt", None) == "/path/to/file.txt"
-
-    with pytest.raises(argparse.ArgumentTypeError):
-        _is_file("/path/to/directory", None)
-
-
-def _test_get_parser():
-    """Test the creation and configuration of the argument parser.
-
-    This function tests the `_get_parser` function by asserting that the returned object is an
-    instance of `argparse.ArgumentParser`, and that it has the expected `prog` and `description`
-    attributes.
-    Additional assertions can be added to test the configuration of the parser.
-    """
-    parser = _get_parser()
-    assert isinstance(parser, argparse.ArgumentParser)
-    assert parser.prog == "cubids"
-    assert parser.description == "Console script for cubids"
-    # Add more assertions for the parser configuration
-
-
-def _test_main():
-    """Test the main function of the CLI.
-
-    This function tests the `_main` function by providing different sets of arguments.
-    It asserts that the function returns the expected exit code (0 or 1) based on the provided
-    arguments.
-    """
-    # Test the main function with valid arguments
-    argv = ["validate", "/path/to/dataset"]
-    assert _main(argv) == 0
-
-    # Test the main function with invalid arguments
-    argv = ["invalid-command", "/path/to/dataset"]
-    assert _main(argv) == 1
-
-    # Test the main function with missing arguments
-    argv = []
-    assert _main(argv) == 1
+from cubids.cli import _is_file, _path_exists
+from cubids.tests.utils import chdir
+
+
+def test_path_exists(tmp_path):
+    """Test whether a given path exists or not."""
+    parser = argparse.ArgumentParser()
+
+    # Test with an existing path
+    existing_path = tmp_path / "existing_file.txt"
+    existing_path.touch()  # Create the file
+    result = _path_exists(str(existing_path), parser)
+    assert result == existing_path.absolute()
+
+    # Test with just filename
+    with chdir(tmp_path):
+        result = _path_exists("existing_file.txt", parser)
+        assert result == existing_path.absolute()
+
+    # Test with a non-existing path
+    non_existing_path = tmp_path / "non_existing_file.txt"
+    with pytest.raises(SystemExit):
+        _path_exists(str(non_existing_path), parser)
+
+    # Test within an argument parser
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    PathExists = partial(_path_exists, parser=parser)
+    parser.add_argument(
+        "existing_folder",
+        type=PathExists,
+        action="store",
+    )
+
+    # Test with an existing path within an argument parser
+    parser.parse_args([str(existing_path)])
+
+    # Test with just filename
+    with chdir(tmp_path):
+        parser.parse_args(["existing_file.txt"])
+
+    # Test with a non-existing path within an argument parser
+    with pytest.raises(SystemExit):
+        parser.parse_args([str(non_existing_path)])
+
+
+def test_is_file(tmp_path):
+    """Test whether a given path exists or not."""
+    parser = argparse.ArgumentParser()
+
+    # Test with an existing path
+    existing_path = tmp_path / "existing_file.txt"
+    existing_path.touch()  # Create the file
+    result = _is_file(str(existing_path), parser)
+    assert result == existing_path.absolute()
+
+    # Test with just filename
+    with chdir(tmp_path):
+        result = _is_file("existing_file.txt", parser)
+        assert result == existing_path.absolute()
+
+    # Test with a non-existing path
+    non_existing_path = tmp_path / "non_existing_file.txt"
+    with pytest.raises(SystemExit):
+        _is_file(str(non_existing_path), parser)
+
+    # Test within an argument parser
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    IsFile = partial(_is_file, parser=parser)
+    parser.add_argument(
+        "existing_file",
+        type=IsFile,
+        action="store",
+    )
+
+    # Test with an existing path within an argument parser
+    parser.parse_args([str(existing_path)])
+
+    # Test with just filename
+    with chdir(tmp_path):
+        parser.parse_args(["existing_file.txt"])
+
+    # Test with a non-existing path within an argument parser
+    with pytest.raises(SystemExit):
+        parser.parse_args([str(non_existing_path)])

cubids/tests/utils.py

@@ -4,6 +4,7 @@
 import json
 import os
 import shutil
+from contextlib import contextmanager
 from pathlib import Path
 
 import nibabel as nb
@@ -80,3 +81,17 @@ def _edit_a_json(json_file):
     metadata["THIS_IS_A_TEST"] = True
     with open(json_file, "w") as metadataw:
         json.dump(metadata, metadataw)
+
+
+@contextmanager
+def chdir(path):
+    """Temporarily change directories.
+
+    Taken from https://stackoverflow.com/a/37996581/2589328.
+    """
+    oldpwd = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(oldpwd)